8FQF: GluA2 flip Q isoform of AMPA receptor

GluA2 flip Q isoform of AMPA receptor in complex with gain-of-function TARP gamma-2, with 150mM NaCl, 330uM CTZ, and 100mM glutamate (Open-Na260). Determined by electron microscopy at 2.29 Å resolution. Released 28 Feb 2024.

Method: Electron microscopy
Resolution: 2.29 Å
Organisms: Rattus norvegicus, Mus musculus
Chains: 8
Atoms: 10,895
Mol. weight: 546.75 kDa
Released: 28 Feb 2024

Explore 8FQF in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8FQF contains 62 α-helices and 40 β-strands across 8 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 9 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	516-518	3
β-strand	521	1	1
α-helix	523-545	23
α-helix	548-550	3
β-strand	551-552	2	2
β-strand	566-567	2	2
α-helix	573-584	12
α-helix	596-624	29
α-helix	785-786	2
β-strand	787	1	3
α-helix	788	1
α-helix	789-791	3
α-helix	793-825	33

Chains B and D: 12 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	508	1
β-strand	509-510	2	4
α-helix	511-512	2
α-helix	516-518	3
β-strand	521	1	5
α-helix	523-545	23
α-helix	548-550	3
β-strand	551	1	6
β-strand	567	1	6
α-helix	573-584	12
α-helix	596-617	22
α-helix	620-623	4
β-strand	628-629	2	4
α-helix	786	1
β-strand	787	1	1
α-helix	788	1
α-helix	790-792	3
α-helix	793-825	33

Chain C: 8 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	516-518	3
β-strand	521	1	7
α-helix	523-545	23
α-helix	548-550	3
β-strand	551-552	2	8
β-strand	566-567	2	8
α-helix	573-584	12
α-helix	596-624	29
α-helix	785-786	2
β-strand	787	1	5
α-helix	788	1
α-helix	789-823	35

Chain E: 5 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	6-29	24
β-strand	34-38	5	11
β-strand	57-61	5	11
β-strand	65-68	4	11
β-strand	77-79	3	11
α-helix	93-104	12
α-helix	106-126	21
α-helix	133-160	28
β-strand	175-176	2	11
α-helix	178-213	36

Chains F and H: 5 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	6-29	24
β-strand	34-38	5	13
β-strand	57-61	5	13
β-strand	65-68	4	13
β-strand	77-79	3	13
α-helix	94-104	11
α-helix	106-128	23
α-helix	133-161	29
β-strand	175-176	2	13
α-helix	178-215	38

Chain G: 6 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	6-29	24
β-strand	34-38	5	12
β-strand	57-61	5	12
β-strand	65-68	4	12
β-strand	77-79	3	12
α-helix	93-104	12
α-helix	106-124	19
α-helix	125-127	3
α-helix	133-160	28
β-strand	175-176	2	12
α-helix	178-213	36

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Glutamate receptor 2	A, B, C, D	protein	889	Rattus norvegicus	P19491 (AlphaFold model)
Voltage-dependent calcium channel gamma-2 subunit	E, F, G, H	protein	336	Mus musculus	O88602 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>8FQF_1 Glutamate receptor 2 (chains A, B, C, D)
MQKIMHISVLLSPVLWGLIFGVSSNSIQIGGLFPRGADQEYSAFRVGMVQFSTSEFRLTP
HIDNLEVANSFAVTNAFCSQFSRGVYAIFGFYDKKSVNTITSFCGTLHVSFITPSFPTDG
THPFVIQMRPDLKGALLSLIEYYQWDKFAYLYDSDRGLSTLQAVLDSAAEKKWQVTAINV
GNINNDKKDETYRSLFQDLELKKERRVILDCERDKVNDIVDQVITIGKHVKGYHYIIANL
GFTDGDLLKIQFGGANVSGFQIVDYDDSLVSKFIERWSTLEEKEYPGAHTATIKYTSALT
YDAVQVMTEAFRNLRKQRIEISRRGNAGDCLANPAVPWGQGVEIERALKQVQVEGLSGNI
KFDQNGKRINYTINIMELKTNGPRKIGYWSEVDKMVVTLTELPSGNDTSGLENKTVVVTT
ILESPYVMMKKNHEMLEGNERYEGYCVDLAAEIAKHCGFKYKLTIVGDGKYGARDADTKI
WNGMVGELVYGKADIAIAPLTITLVREEVIDFSKPFMSLGISIMIKKPQKSKPGVFSFLD
PLAYEIWMCIVFAYIGVSVVLFLVSRFSPYEWHTEEFEDGRETQSSESTNEFGIFNSLWF
SLGAFMQQGCDISPRSLSGRIVGGVWWFFTLIIISSYTANLAAFLTVERMVSPIESAEDL
SKQTEIAYGTLDSGSTKEFFRRSKIAVFDKMWTYMRSAEPSVFVRTTAEGVARVRKSKGK
YAYLLESTMNEYIEQRKPCDTMKVGGNLDSKGYGIATPKGSSLGTPVNLAVLKLSEQGVL
DKLKNKWWYDKGECGAKDSGSKEKTSALSLSNVAGVFYILVGGLGLAMLVALIEFCYKSR
AEAKRMKVAKNPQNINPSSSQNSQNFATDYKDDDDKEGYNVYGIESVKI

Sequence of entity 2 (E, F, G, H), FASTA

>8FQF_2 Voltage-dependent calcium channel gamma-2 subunit (chains E, F, G, H)
MGLFDRGVQMLLTTVGAFAAFSLMTIAVGTDYWLYSRGVCKTKSVSENETSEENEEVMTH
SGLWRTCCLEGNFKGLCKQIDHFPEDADYEADTAEYFLRAVRASSIFPILSVILLFMGGL
CIAASEFYKTRHNIILSAGIFFVSAGLSNIIGIIVYISANAGDPSKSDSKKNSYSYGWSF
YFGALSFIIAEMVGVLAVHMFIDRHKQLRATARATDYLQASAITRIPSYRYRYQRRSRSS
SRSTEPSHSRDASPVGVKGFNTLPSTEISMYTLSRDPLKAATTPTATYNSDRDNSFLQVH
NCIQKDSKDSLHANTANRRTTPVGGRGGTETSQAPA

Primary citation

The open gate of the AMPA receptor forms a Ca 2+ binding site critical in regulating ion transport. Nakagawa, T., Wang, X.T., Miguez-Cabello, F.J. et al. Nat Struct Mol Biol (2024) 31:688-700. DOI 10.1038/s41594-024-01228-3 · PubMed

Other PDB entries of the same protein (UniProt P19491 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6YK4 1.0 Å, Structure of the AMPA receptor GluA2o ligand-binding domain (S1S2J) in complex with the…
5NG9 1.15 Å, Crystal structure of the GluA2 ligand-binding domain (S1S2J) in complex with agonist…
6YK5 1.15 Å, Structure of the AMPA receptor GluA2o ligand-binding domain (S1S2J) in complex with the…
6YK3 1.2 Å, Structure of the AMPA receptor GluA2o ligand-binding domain (S1S2J) in complex with the…
5JEI 1.23 Å, Crystal structure of the GluA2 LBD in complex with FW
4IGT 1.24 Å, Crystal structure of the GluA2 ligand-binding domain (S1S2J) in complex with the agonist…
4YU0 1.26 Å, Crystal structure of a tetramer of GluA2 TR mutant ligand binding domains bound with…
5NIH 1.3 Å, Crystal structure of the GluA2 ligand-binding domain (S1S2J) in complex with agonist…
1MQI 1.35 Å, Crystal Structure of the GluR2 Ligand Binding Core (S1S2J) in Complex with…
5FTI 1.35 Å, Crystal structure of the GluA2 K738M-T744K LBD in complex with glutamate (lithium form)
4U21 1.39 Å, GluA2flip sLBD complexed with FW and (R,R)-2b crystal form E
4FAT 1.4 Å, Ligand-binding domain of GluA2 (flip) ionotropic glutamate receptor in complex with an…

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